4.8 Article

Confinement anisotropy drives polar organization of two DNA molecules interacting in a nanoscale cavity

Related references

Note: Only part of the references are listed.
Review Chemistry, Multidisciplinary

Genome-in-a-Box: Building a Chromosome from the Bottom Up

Anthony Birnie et al.

Summary: Chromosome structure and dynamics play a crucial role in gene expression and inheritance. Methods such as GenBox provide a way to study chromosomes in vitro, bridging the gap between top-down experiments on live cells and bottom-up single-molecule studies.

ACS NANO (2021)

Article Chemistry, Medicinal

Heterologous Protein Expression Favors the Formation of Protein Aggregates in Persister and Viable but Nonculturable Bacteria

Olivia Goode et al.

Summary: The study found that heterologous protein expression promotes the formation of protein aggregates, and persister and viable but nonculturable cells are more likely to contain protein aggregates and downregulate the expression of heterologous proteins. These aggregates are more basic compared to the rest of the cell, indicating a strong link between antibiotic treatments, protein aggregation, and pH regulation.

ACS INFECTIOUS DISEASES (2021)

Article Microbiology

The Dynamic Transition of Persistence toward the Viable but Nonculturable State during Stationary Phase Is Driven by Protein Aggregation

Liselot Dewachter et al.

Summary: Decades of research into bacterial persistence has been unable to fully characterize this antibiotic-tolerant phenotype, thereby hampering the development of therapies effective against chronic infections. Although some active persister mechanisms have been identified, the prevailing view is that cells become persistent because they enter a dormant state. We therefore characterized starvation-induced dormancy in Escherichia coli. Our findings indicate that dormancy develops gradually; persistence strongly increases during stationary phase and decreases again as persisters enter the viable but nonculturable (VBNC) state. Importantly, we show that dormancy development is tightly associated with progressive protein aggregation, which occurs concomitantly with ATP depletion during starvation. Persisters contain protein aggregates in an early developmental stage, while VBNC cells carry more mature aggregates. Finally, we show that at least one persister protein, ObgE, works by triggering aggregation, even at endogenous levels, and thereby changing the dynamics of persistence and dormancy development. These findings provide evidence for a genetically controlled, gradual development of persisters and VBNC cells through protein aggregation. IMPORTANCE While persistence and the viable but nonculturable (VBNC) state are currently investigated in isolation, our results strongly indicate that these phenotypes represent different stages of the same dormancy program and that they should therefore be studied within the same conceptual framework. Moreover, we show here for the first time that the dynamics of protein aggregation perfectly match the onset and further development of bacterial dormancy and that different dormant phenotypes are linked to different stages of protein aggregation. Our results thereby strongly hint at a causal relationship between both. Because many conditions known to trigger persistence are also known to influence aggregation, it is tempting to speculate that a variety of different persister pathways converge at the level of protein aggregation. If so, aggregation could emerge as a general principle that underlies the development of persistence which could be exploited for the design of antipersister therapies.
Article Chemistry, Physical

Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement

James M. Polson et al.

Summary: Motivated by recent nanofluidics experiments, the study investigates the conformation, organization, and dynamics of two polymer chains confined to a single box-like cavity using Brownian dynamics and Monte Carlo simulations. The behavior of the system approaches that of an isolated polymer in a slit geometry as the box width increases. Polymer size reduction is primarily due to confinement, while polymer diffusion and internal motion are significantly affected by inter-polymer crowding.

SOFT MATTER (2021)

Review Microbiology

Protein aggregation in bacteria

Frederic D. Schramm et al.

FEMS MICROBIOLOGY REVIEWS (2020)

Article Biochemistry & Molecular Biology

Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells

Charlene Planchenault et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

Article Physics, Applied

Particle tracking of nanoparticles in soft matter

Katie A. Rose et al.

JOURNAL OF APPLIED PHYSICS (2020)

Article Biophysics

High-Copy-Number Plasmid Segregation-Single-Molecule Dynamics in Single Cells

Tai-Ming Hau et al.

BIOPHYSICAL JOURNAL (2019)

Article Chemistry, Multidisciplinary

Probing Inhomogeneous Diffusion in the Microenvironments of Phase-Separated Polymers under Confinement

Marjan Shayegan et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Biochemistry & Molecular Biology

Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

Fabai Wu et al.

CURRENT BIOLOGY (2019)

Article Biology

Bacterial ageing in the absence of external stressors

Urszula Lapinska et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2019)

Review Physics, Applied

Novel physics arising from phase transitions in biology

Chiu Fan Lee et al.

JOURNAL OF PHYSICS D-APPLIED PHYSICS (2019)

Article Chemistry, Physical

Diffusion of nanoparticles within a semidilute polyelectrolyte solution

Kavindya K. Senanayake et al.

SOFT MATTER (2019)

Article Chemistry, Multidisciplinary

Dynamics of Nanoparticles in Entangled Polymer Solutions

Pooja Nath et al.

LANGMUIR (2018)

Article Polymer Science

Compression of Nanoslit Confined Polymer Solutions

Yue Qi et al.

MACROMOLECULES (2018)

Article Physics, Multidisciplinary

Self-Avoiding Wormlike Chain Confined in a Cylindrical Tube: Scaling Behavior

Jeff Z. Y. Chen

PHYSICAL REVIEW LETTERS (2018)

Article Biochemistry & Molecular Biology

Protein aggregates encode epigenetic memory of stressful encounters in individual Escherichia coli cells

Sander K. Govers et al.

PLOS BIOLOGY (2018)

Article Chemistry, Physical

Pneumatically Controlled Nanofluidic Devices for Contact-Free Trapping and Manipulation of Nanoparticles

Michael Adrian Gerspach et al.

PARTICLE & PARTICLE SYSTEMS CHARACTERIZATION (2018)

Article Physics, Fluids & Plasmas

Evidence for the extended de Gennes regime of a semiflexible polymer in slit confinement

Guo Kang Cheong et al.

PHYSICAL REVIEW E (2018)

Article Physics, Fluids & Plasmas

Wall depletion length of a channel-confined polymer

Guo Kang Cheong et al.

PHYSICAL REVIEW E (2017)

Review Biochemistry & Molecular Biology

The Continuing Mystery of Lipid Rafts

Ilya Levental et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Article Multidisciplinary Sciences

Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment

Christian L. Vestergaard et al.

NATURE COMMUNICATIONS (2016)

Review Cell Biology

Bacterial Chromosome Organization and Segregation

Anjana Badrinarayanan et al.

ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 31 (2015)

Article Chemistry, Physical

Polymer segregation under confinement: Free energy calculations and segregation dynamics simulations

James M. Polson et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Genetics & Heredity

Mechanisms of plasmid segregation: Have multicopy plasmids been overlooked?

Samuel Million-Weaver et al.

PLASMID (2014)

Article Multidisciplinary Sciences

Convex lens-induced nanoscale templating

Daniel J. Berard et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemical Research Methods

Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect

Anne-Sophie Coquel et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Mathematics, Applied

New development in freefem++

F. Hecht

JOURNAL OF NUMERICAL MATHEMATICS (2012)

Article Chemistry, Multidisciplinary

Mass Action at the Single-Molecule Level

Min Ju Shon et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Polymer Science

Intrachain Ordering and Segregation of Polymers under Confinement

Youngkyun Jung et al.

MACROMOLECULES (2012)

Article Physics, Multidisciplinary

Experimental Observations of Dynamic Critical Phenomena in a Lipid Membrane

Aurelia R. Honerkamp-Smith et al.

PHYSICAL REVIEW LETTERS (2012)

Review Physics, Multidisciplinary

DNA confinement in nanochannels: physics and biological applications

Walter Reisner et al.

REPORTS ON PROGRESS IN PHYSICS (2012)

Article Biotechnology & Applied Microbiology

Radius of Gyration of Plasmid DNA Isoforms From Static Light Scattering

David R. Latulippe et al.

BIOTECHNOLOGY AND BIOENGINEERING (2010)

Article Polymer Science

Revisiting the Conformation and Dynamics of DNA in Slitlike Confinement

Jing Tang et al.

MACROMOLECULES (2010)

Review Microbiology

Entropy as the driver of chromosome segregation

Suckjoon Jun et al.

NATURE REVIEWS MICROBIOLOGY (2010)

Review Microbiology

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

Shane C. Dillon et al.

NATURE REVIEWS MICROBIOLOGY (2010)

Article Multidisciplinary Sciences

Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel

Ce Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

Clifford P. Brangwynne et al.

SCIENCE (2009)

Article Physics, Multidisciplinary

Conformation and dynamics of DNA confined in slitlike nanofluidic channels

Douwe Jan Bonthuis et al.

PHYSICAL REVIEW LETTERS (2008)

Article Multidisciplinary Sciences

Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation

Ariel B. Lindner et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Microbiology

Existence of abnormal protein aggregates in healthy Escherichia coli cells

Etienne Maisonneuve et al.

JOURNAL OF BACTERIOLOGY (2008)

Article Multidisciplinary Sciences

Entropy-driven spatial organization of highly confined polymers: Lessons for the bacterial chromosome

Suckjoon Jun et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Materials Science, Ceramics

High speed anisotropic etching of Pyrex® for microsystems applications

Abhijat Goyal et al.

JOURNAL OF NON-CRYSTALLINE SOLIDS (2006)

Review Biochemistry & Molecular Biology

Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes

ES Egan et al.

MOLECULAR MICROBIOLOGY (2005)

Review Biochemistry & Molecular Biology

Archaea with square cells

AE Walsby

TRENDS IN MICROBIOLOGY (2005)

Article Physics, Multidisciplinary

Anomalous diffusion probes microstructure dynamics of entangled F-actin networks

IY Wong et al.

PHYSICAL REVIEW LETTERS (2004)